2AFA | pdb_00002afa

Crystal Structure of putative NAG isomerase from Salmonella typhimurium

PDB DOI: https://doi.org/10.2210/pdb2AFA/pdb

Classification: ISOMERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-07-25 Released: 2005-08-16
Deposition Author(s): Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.246 (Depositor), 0.240 (DCC)
R-Value Work:
0.207 (Depositor), 0.205 (DCC)
R-Value Observed:
0.207 (Depositor)

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This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of putative NAG isomerase from Salmonella typhimurium

Kumaran, D., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 296.48 kDa
Atom Count: 20,569
Modeled Residue Count: 2,448
Deposited Residue Count: 2,550
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAG isomerase	A, B, C, D, E A, B, C, D, E, F	425	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 9 Gene Names: yihS EC: 5.3.1.31
UniProt
Find proteins for Q8ZKT7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZKT7 Go to UniProtKB: Q8ZKT7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZKT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.246 (Depositor), 0.240 (DCC)
R-Value Work: 0.207 (Depositor), 0.205 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.933	α = 106.81
b = 91.14	β = 103.52
c = 95.102	γ = 111.79

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-08-16

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2005-08-16
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.